Setup
Load libraries
library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6 ✔ purrr 0.3.4
## ✔ tibble 3.1.8 ✔ dplyr 1.0.9
## ✔ tidyr 1.2.0 ✔ stringr 1.4.0
## ✔ readr 2.1.2 ✔ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
library(cowplot)
library(latex2exp)
library(ggside)
## Registered S3 method overwritten by 'ggside':
## method from
## +.gg ggplot2
library(ggsci)
library(plotly)
##
## Attaching package: 'plotly'
##
## The following object is masked from 'package:latex2exp':
##
## TeX
##
## The following object is masked from 'package:ggplot2':
##
## last_plot
##
## The following object is masked from 'package:stats':
##
## filter
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## The following object is masked from 'package:graphics':
##
## layout
library(ggdist)
Load from cache
co_registered <- readRDS("cache/co_registered.RDS")
cd_pc_data <- readRDS("cache/cd_pc_data.RDS")
Colors
organism_colors <- c("#008c54", "#ffaa00")
Plot
Co-registered
p_co_registered <- co_registered %>%
# Plot it!
ggplot(
aes(x = at2H_percent,
y = cd_pc,
color = as.factor(f_l),
group = organism.x,
label = cell_id
)
) +
geom_point(
alpha = 0.5,
size = 2
) +
geom_abline(
slope = 1,
linetype = "dashed",
color = "gray",
alpha = 1,
) +
stat_smooth(
formula = y ~ x,
#formula = y ~ splines::bs(x, 3),
size = 0.5,
method = 'lm'
) +
facet_wrap(vars(organism.x)) +
coord_cartesian(
xlim = c(0,50),
ylim = c(0,50)
) +
scale_color_viridis_d(end = 0.9) +
theme_bw() +
labs(
x = TeX("$^2F$ (atom %)"),
y = "CD% (Raman)",
color = TeX("Label Strength $^2F$ (atom %)")
) +
theme(
legend.position = "bottom",
ggside.panel.scale = 2
)
p_co_registered
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).

Plotly
ggplotly(p = p_co_registered)
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: `gather_()` was deprecated in tidyr 1.2.0.
## Please use `gather()` instead.
## Warning: Detected the use of `TeX()`, but mathjax has not been specified. Try
## running `config(.Last.value, mathjax = 'cdn')`
CD FL
p_cd_fl <- co_registered %>%
filter(!is.na(f_l)) %>%
ggplot(
aes(x = f_l,
y = cd_pc,
color = organism.x
)
) +
labs(
x = latex2exp::TeX("$^2F$ Growth Water"),
y = latex2exp::TeX("$^2F_{Raman}$")
) +
facet_wrap(
vars(organism.x),
scales = "free") +
geom_abline(
slope = 1,
linetype = "dashed",
color = "gray",
alpha = 1,
) +
geom_point(
alpha = 0.5,
position = position_jitter(width = 2)
) +
ggdist::stat_pointinterval(
position = position_nudge(x = 0.2),
color = "black"
) +
scale_color_manual(values = organism_colors) +
scale_x_continuous(
limits = c(0, 55),
breaks = c(0, 10, 20, 30, 40, 50)
) +
scale_y_continuous(
limits = c(0, 55),
breaks = c(0, 10, 20, 30, 40, 50)
) +
theme_classic() +
theme(
legend.position = "NA",
strip.background = element_blank()
)
p_cd_fl
## Warning: Removed 48 rows containing missing values (geom_point).

2F FL
p_2f_fl <- co_registered %>%
filter(!is.na(f_l)) %>%
ggplot(
aes(x = f_l,
y = at2H_percent,
color = organism.x
)
) +
facet_wrap(vars(organism.x), scales = "free") +
geom_abline(
slope = 1,
linetype = "dashed",
color = "gray",
alpha = 1,
) +
geom_point(
alpha = 0.5,
position = position_jitter(width = 2)
) +
scale_color_manual(values = organism_colors) +
scale_x_continuous(
limits = c(0, 55),
breaks = c(0, 10, 20, 30, 40, 50)
) +
scale_y_continuous(
limits = c(0, 55),
breaks = c(0, 10, 20, 30, 40, 50)
) +
labs(
x = latex2exp::TeX("$^2F$ Growth Water"),
y = latex2exp::TeX("$^2F_{nanoSIMS}$")
) +
ggdist::stat_pointinterval(
position = position_nudge(x = 0.2),
color = "black"
) +
theme_classic() +
theme(
legend.position = "NA",
strip.background = element_blank()
)
p_2f_fl
## Warning: Removed 35 rows containing missing values (geom_point).

Cowplot: CD-FL and 2F-FL
cowplot::plot_grid(
p_cd_fl,
p_2f_fl,
ncol = 1
)
## Warning: Removed 38 rows containing missing values (geom_point).
## Warning: Removed 36 rows containing missing values (geom_point).

2R FL
co_registered %>%
filter(!is.na(f_l)) %>%
ggplot(
aes(x = as.factor(f_l),
y = `Ratio_2Hx1H`,
color = organism.x
)
) +
facet_wrap(vars(organism.x)) +
geom_point(
alpha = 0.25
) +
scale_color_manual(values = organism_colors) +
labs(
x = latex2exp::TeX("$^2F$ Growth Water"),
y = latex2exp::TeX("$^2R_{nanoSIMS}$")
) +
theme_classic() +
theme(
legend.position = "NA",
strip.background = element_blank()
)

Raman spectrum
cd_pc_data %>% filter(cell_id == "Mb_50_18_38") %>%
ggplot(aes(
x = wavenumber_cm,
y = intensity
)) +
geom_line() +
theme_minimal()
